INSDC

Controlled vocabulary for /type_material qualifier

Type material is a taxonomic term that ties formal names to specimens that can be used for identification and description of a new taxonomic entity.

Reference: Nucleic Acids Res. 2015 Jan;43(Database issue):D1086-98. doi: 10.1093/nar/gku1127.

INSDC will automatically populate this qualifier from the NCBI taxonomy database to flag sequences of form type in the INSDC databases (ENA/GenBank/DDBJ).

The controlled vocabulary used for various types can be found in the below table.

 

Type Name Synonym Nomenclatures* Comment
type material   BZ basic type material – this is default type (except for Archaea and Bacteria)
type strain   P deposited in at least two different culture collections – default type for Archaea and Bacteria
reference material   BZ non-type material designated for reference purposes (except for Archaea and Bacteria)
reference strain   P non-type material designated for reference purposes (for Archaea and Bacteria)
neotype strain   P replacement culture for a type that has been lost
holotype   BZ single name-bearing type specimen
isotype   B duplicate specimen of the holotype
paratype   BZ other specimens designated in the original type series
neotype   BZ single name-bearing specimen designated when holotype is lost
epitype   B other specimen designated in subsequent type series
syntype   BZ one of a name-bearing series of type specimens
isosyntype   B duplicate specimen of a syntype
lectotype   BZ syntype subsequently designated as the single name-bearing type
paralectotype   Z syntype not subsequently designated as lectotypes
hapantotype   Z protist assemblage collectively designated as holotype
allotype   Z designated type specimen of opposite sex to the holotype
isoparatype   B duplicate specimen of a paratype
isoneotype   B duplicate specimen of a neotype
isolectotype   B duplicate specimen of a lectotype
isoepitype   B duplicate specimen of an epitype
culture from reference   BZ living eukaryotic culture derived from reference material
culture from type material ex-type BZ living eukaryotic culture derived from type material
culture from paratype ex-paratype BZ living eukaryotic culture derived from paratype
culture from neotype ex-neotype BZ living eukaryotic culture derived from neotype
culture from lectotype ex-lectotype BZ living eukaryotic culture derived from lectotype
culture from hapantotype   Z living eukaryotic culture derived from hapantotype
culture from isosyntype ex-isosyntype B living eukaryotic culture derived from isosyntype
culture from isotype ex-isotype B living eukaryotic culture derived from isotype
culture from isoparatype ex-isoparatype B living eukaryotic culture derived from isoparatype
culture from isoneotype ex-isoneotype B living eukaryotic culture derived from isoneotype
culture from isolectotype ex-isolectotype B living eukaryotic culture derived from isolectotype
culture from holotype ex-holotype BZ living eukaryotic culture derived from holotype
culture from epitype ex-epitype B living eukaryotic culture derived from epitype
culture from syntype ex-syntype BZ living eukaryotic culture derived from syntype
culture from isoepitype ex-isoepitype B living eukaryotic culture derived from isoepitype
pathotype strain   P strain designated as the type for the associated pathovar

 

*NOTE: Nomenclature letter coding is explained in the following table:                      

B               International Code of Nomenclature for algae, fungi, and plants  

P               International Code of Nomenclature of Prokaryotes          

V               International Committee on Taxonomy of Viruses               

Z               The International Code of Zoological Nomenclature